This script runs the Color to Alpha filter on all layers in an image. The preview image shows the left part of the animation with black left in and the right side shows it with the black removed.
You choose the color to be transparent and the script does the rest.
Download the zip file, open the zip file by double-clicking on it and copy/paste the script to your GIMP scripts folder (ie...C:\Program Files\GIMP-2.0\share\gimp\2.0\scripts). Refresh your scripts and you're ready to go. The script can be located under the Colors > Color to Alpha All Layers...
Let me know if you have any trouble or need additional information.
(Just kidding :3)